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Even though the problem is actually with the Pi I2C hardware, it can be worked around. This is a changed to the slave CPU, not the Pi. Putting a time delay in the Wire library twi.c allows talking to Arduino-likes from the Raspberry Pi on I2C. My atmega328p CPU is @ 8 MHz so perhaps this needs to be tweaked for 16 MHz cases (normal Arduino). Anyway, this bandaid completely stopped the problem (twi.c, in SIGNAL(TWI_vect) routine):